Dear Amber users
I am using Amber12. I am noticing one error very recently, which was not
happening earlier. I am trying to perform minimisation and equilibration of
a protein-inhibitor complex. When I am using the command tleap -s -f leap.in to
run LEaP, I am getting the following error:
-I: Adding /usr/local/bin/amber12//dat/leap/prep to search path.
-I: Adding /usr/local/bin/amber12//dat/leap/lib to search path.
-I: Adding /usr/local/bin/amber12//dat/leap/parm to search path.
-I: Adding /usr/local/bin/amber12//dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leap.in.
Welcome to LEaP!
Sourcing: ./leap.in
: not foundpen file leaprc.ff99SB
: not foundpen file leaprc.gaff
: not foundpen file tmc.frc
: not foundpen file tmc.prep
: not foundpen file min3.pdb
solvateBox: Argument #1 is type String must be of type: [unit]
usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
check: Argument #1 is type String must be of type: [unit molecule residue
atom]
usage: check <unit> [parmset]
charge: Argument #1 is type String must be of type: [unit molecule residue
atom list]
usage: charge <object>
addIons: Argument #1 is type String must be of type: [unit]
addIons unit ion1 #ion1 [ion2 #ion2]
UNIT _unit_
UNIT _ion1_
NUMBER _#ion1_
UNIT _ion2_
NUMBER _#ion2_
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addions, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.
savePdb: Argument #1 is type String must be of type: [unit]
usage: savePdb <object> <filename>
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage: saveAmberParm <unit> <topologyfile> <coordfile>
ERROR: syntax error
ERROR: syntax error
>
However, when I am doing it separately, line by line, as in, tleap
source leaprc.ff99SB and so on, it is working fine and proper topology and
crd files are generated.
I wonder what is happening that is preventing tleap -s -f from working for
me.
My leap input file is:
source leaprc.ff99SB
source leaprc.gaff
mod1 = loadAmberParams tmc.frc
loadAmberPrep tmc.prep
ACHE = loadpdb min3.pdb
solvatebox ACHE TIP3PBOX 9.0
check ACHE
charge ACHE
addions ACHE Cl- 0
savepdb ACHE tmc_wat.pdb
saveAmberParm ACHE tmc_wat.top tmc_wat.crd
quit
Needless to say, all relevant files are in the same working directory.
Any help would be greatly appreciated. Thanks
Suchetana Gupta
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Received on Tue Jul 15 2014 - 02:30:03 PDT
